i think it will be the baffles for sure!
ive got a Autech Can on my car, and after a full track day on a hot day, it has had a smoky exhaust for a good 1-2hours after. i remember the first time i went to the Creek, it was a 30 odd deg day, my oil temp got up to 130deg at one stage, therefore would have been thining right out, when i got home that night i had my car just idling out the front of my garage and she was puffing a heap of smoke, i thought the turbo seals where gone or somthing, took it for a cruise no boost drive by the time i was back, it was all normal again. At the time my Autech was plumbed back into the intake, its now Atmo.....
Change the baffles man, let us no how you go!